His running mate, William Ruto, also faces ICC charges at The Hague, in the Netherlands.
Former Agriculture Minister William Ruto and radio journalist Joshua Arap Sang face similar charges.
CNN: Kenyan leaders to stand trial on human rights violations
"It is the decision of the court that (Kenyatta and Ruto) were validly elected, " the ruling said.
The decision "is meant to deny us a first-round win, " Ruto was quoted as saying by The Standard newspaper.
Mr Kibaki was backed by Mr Kenyatta, while Mr Ruto supported Mr Odinga.
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Deputy President William Ruto noted that he and Kenyatta won in the first round of voting despite the U.S. warning.
The petition described Mr Kenyatta and Mr Ruto as the "glue" that bound "the country during the elections and transition period".
Mr Kenyatta and his running mate, William Ruto, are expected to be sworn in as president and vice-president on 9 April.
BBC: Kenya Supreme Court upholds Uhuru Kenyatta election win
William Ruto, Kenyatta's running mate, on Tuesday had also blamed "foreign missions" for swaying the electoral commission on its ballot decision.
This week Mr Ruto was cleared of corruption in a separate local case that had got him suspended from the cabinet.
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His running mate, William Ruto, also faces ICC charges at The Hague.
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Mr Kenyatta is an ethnic Kikuyu while Mr Ruto is a Kalenjin.
Mr Uhuru and Mr Ruto - rivals in December 2007 poll - are due to go on trial in April in The Hague.
The case has also exposed the extent of alarm from Western nations at the prospect of Mr Kenyatta and Mr Ruto being elected.
Kenyatta and Deputy President-elect William Ruto both face charges that they helped orchestrate the 2007-08 postelection violence in which more than 1, 000 people died.
Mr Kenyatta's running mate William Ruto, who is also facing a trial at the ICC, said foreign embassies may have influenced such a decision.
Kenyatta's running mate, William Ruto, also faces charges at the ICC.
The ICC has agreed to postpone Mr Ruto's trial by a month until May after his lawyers complained of not having enough time to prepare his defence.
Mr Kenyatta and Mr Ruto present themselves as victims of a Western conspiracy, and portray Mr Odinga as a stooge of the West and architect of their indictment.
Mr Kenyatta's running mate, William Ruto, also faces similar charges.
Mr Kenyatta's running mate, William Ruto, has also been indicted.
Ruto also said he still plans to run for president.
CNN: Kenyan leaders to stand trial on human rights violations
Earlier this month two ex-Kenyan ministers William Ruto and Henry Kosgey, as well as radio executive Joshua Arap Sang, appeared to face pre-trial hearings over their alleged part in the violence.
But the Supreme Court's unanimous decision, read out by Chief Justice Willy Mutunga, said the election was "conducted in compliance with the constitution and the law" and that Kenyatta and Ruto were legally elected.
Police Inspector General David Kimaiyo said the leaflets found in Kisumu, a city in western Kenya, were inciting Luo residents to chase away people from the Kikuyu and Kalenjin communities, who traditionally support Mr Kenyatta and Mr Ruto.
The ICC case against four Kenyans - including Mr Kenyatta and Mr Ruto - is taking centre stage in the elections and was an issue that featured prominently in the first presidential debate last week between the eight leading candidates for the post.
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